New Method for Determining Protein Structure is 20 Times More Efficient

Feb 18, 2014

Research involving scientists from Trinity
College Dublin has made a major breakthrough that will streamline the process
used to determine the structure of proteins in cell membranes. The development
of a new method, and a specialist device to implement the most complex part of
the method, should have a major impact on drug-related research.

Over 50% of drugs on the market target cell
membrane proteins. It is vital that researchers have high-resolution, 3-D
structures of these cell membrane proteins because such ‘physiological
roadmaps’ allow better interpretation of their functional mechanisms. This knowledge can in turn pinpoint weaknesses that can be exploited by drugs
specifically designed to act with high selectivity and potency.

Proteins in cell membranes are also vital for
the everyday functioning of complex cellular processes. They act as
transporters to ensure that specific molecules enter and leave our cells, as
signal interpreters important in decoding messages and initiating responses,
and as agents that speed up appropriate responses. As such, it is vital that we
know as much about them as possible.

The major challenge facing researchers is the
production of large membrane protein crystals. These crystals are used to
determine 3-D structure in a complicated process that involves X-rays being
fired at them to produce ‘diffraction’ patterns, which can then be used as
‘unique structural fingerprints’ of the proteins.

A research group led by Professor of Membrane
Structural and Functional Biology at Trinity, Martin Caffrey,
developed a high-throughput method for growing membrane protein crystals that
makes use of the ‘Lipid Cubic Phase’ (LCP). The LCP uses a fat-based media to
grow these crystals in. Professor Brian Kobilka was awarded his share in the
2012 Nobel Prize in Chemistry, in part for work that made use of the LCP.

Recently, a new method for determining
membrane protein structures that uses an X-ray-free electron laser showed great promise.
However, it required huge numbers of protein crystals to generate a clear
picture of their structure as only 1 in 10,000 was hit in a way that produced
useable data. In the breakthrough, Professor Caffrey, as part of a large team
of scientists, used the fat-based LCP media in which the protein crystals were
grown to jet them across the laser at a relatively slow pace. This slower pace
translated into a vastly improved ‘hit rate’, which in turn provided a more
efficient profiling of the protein structure.

In order for the new method to work, the
researchers needed to create a device to stream cell membrane protein crystals
in the LCP media at a consistent rate. Termed the ‘LCP injector’, their new
device, which resembles a high-tech syringe, is able to adjust the speed of LCP
release as required to minimise sample wastage.

Determining the structure of cell membrane proteins
has long been seen as a laborious, time consuming, and extremely expensive
necessity for medical and therapeutic research. But the new method could change
that after the researchers showed it consumed 20 times less protein than the
method most commonly used beforehand.

With reference to the research just published
in the high-profile journal, Nature Communications, Professor of
Membrane Structural and Functional Biology at Trinity, Martin Caffrey, said:
“This collaborative work represents a tremendous breakthrough that should
greatly improve the efficiency with which research is conducted into
determining membrane protein structure.”

“The LCP injector shoots the LCP media out at
a consistency resembling toothpaste, but at a rate and stream width that must
remain highly controlled. Achieving that represented a real challenge and it’s
very exciting that the final device works so beautifully. Our work will have
major applications in the field of drug research and should make it much more
efficient and less costly to determine the structure of proteins of interest.”